We have examined the utility of a
graph-theoretic algorithm for building comparative RNA models. The method uses
a maximum weighted matching algorithm to find the optimal set of base-pairs
given the mutual information for all pairs of alignment positions. In all cases
examined, the technique generated models similar to those based on conventional
comparative analysis. Any set of pairwise interactions can be suggested
including pseudoknots. Here we describe the details of the method and
demonstrate its implementation on tRNA where many secondary and tertiary
base-pairs are accurately predicted. We also examine the usefulness of the
method for the identification of shared structural features in families of RNAs
isolated by artificial selection methods such as SELEX.

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